Jason Amsden

Research Interests

My area of interest is in the application of computational and compressive techniques to improve spectroscopic instrument design. Spectroscopic measurements are a convolution of the instrument response and the desired spectrum. Conventional spectroscopic instruments are designed such that the instrument response is a delta function and the measurements are essentially the desired spectrum. However, this design approach can limit the spectrometer performance. I use a different approach by designing the system response to maximize parameters of interest such as throughput and resolution, and then computationally deconvolve the system response from the measurements to achieve a spectrum – thus improving instrument performance.

Education

• Ph.D. Boston University, 2008

Positions

• Associate Research Professor in the Department of Electrical and Computer Engineering

Publications

• Aloui T, Vyas R, Francini S, Serpa RB, Horvath KL, Keogh J, et al. Spectral Reconstruction Improvement in a Cycloidal Coded-Aperture Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2024 May;35(5):855–61.
• von Windheim T, Gilchrist KH, Parker CB, Hall S, Carlson JB, Stokes D, et al. Proof-of-Concept Vacuum Microelectronic NOR Gate Fabricated Using Microelectromechanical Systems and Carbon Nanotube Field Emitters. Micromachines. 2023 Apr;14(5):973.
• Aloui T, Serpa RB, Abboud N, Horvath KL, Keogh J, Parker CB, et al. A super-resolution proof of concept in a cycloidal coded aperture miniature mass spectrometer. Rapid communications in mass spectrometry : RCM. 2023 Jan;e9477.
• Horvath KL, Piacentino EL, Serpa RB, Aloui T, Vyas R, Zhilichev Y, et al. Design considerations for a cycloidal mass analyzer using a focal plane array detector. Journal of mass spectrometry : JMS. 2022 Jul;57(7):e4874.
• Serpa RB, Piacentino EL, Horvath KL, Aloui T, Zhilichev Y, Parker CB, et al. Virtual-slit focusing in a cycloidal mass spectrometer – A proof of concept. International Journal of Mass Spectrometry. 2021 Dec 1;470.
• Piacentino EL, Serpa RB, Horvath KL, Vyas R, Aloui T, Parker CB, et al. The Long Neglected Cycloidal Mass Analyzer. Analytical chemistry. 2021 Aug;93(33):11357–63.
• Vyas R, Aloui T, Horvath K, Herr PJ, Kirley MP, Parker CB, et al. Improving the Performance of a Cycloidal Coded-Aperture Miniature Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2021 Feb;32(2):509–18.
• Vyas R, Herr PJ, Aloui T, Horvath K, Kirley MP, Parker CB, et al. Comparison of thermionic filament and carbon nanotube field emitter-based electron ionization sources in cycloidal coded aperture mass analyzers. International Journal of Mass Spectrometry. 2020 Nov 1;457.
• DiDona S, Russell Z, Amsden J, Parker C, Glass J, Gehm M. A novel sector mass spectrograph design for high-order coded aperture Mass Spectrometry with stigmatic aberration correction. International Journal of Mass Spectrometry. 2020 Sep 1;455.
• Aloui T, Kirley MP, Vick E, Hilton A, Colon P, Kim W, et al. High current density electron emission from an electrodeposited metal nanowire array. Journal of Vacuum Science and Technology B. 2020 Jul 1;38(4).
• Amsden JJ, Herr PJ, Vyas R, Horvath K, Kirley MP, Li X, et al. Prototype coded aperture miniature mass spectrometer for environmental sensing. In: AQM 2019 - Air Quality Measurement Methods and Technology Conference 2019. 2019.
• Amsden JJ, Herr PJ, Vyas R, Horvath K, Kirley MP, Li X, et al. Prototype coded aperture miniature mass spectrometer for environmental sensing. In: AQM 2019 - Air Quality Measurement Methods and Technology Conference 2019. 2019.
• Amsden JJ, Herr PJ, Landry DMW, Kim W, Vyas R, Parker CB, et al. Proof of Concept Coded Aperture Miniature Mass Spectrometer Using a Cycloidal Sector Mass Analyzer, a Carbon Nanotube (CNT) Field Emission Electron Ionization Source, and an Array Detector. Journal of the American Society for Mass Spectrometry. 2018 Feb;29(2):360–72.
• Landry DMW, Kim W, Amsden JJ, Di Dona ST, Choi H, Haley L, et al. Effects of Magnetic and Electric Field Uniformity on Coded Aperture Imaging Quality in a Cycloidal Mass Analyzer. Journal of the American Society for Mass Spectrometry. 2018 Feb;29(2):352–9.
• Radauscher EJ, Parker CB, Gilchrist KH, Di Dona S, Russell ZE, Hall SD, et al. A miniature electron ionization source fabricated using microelectromechanical systems (MEMS) with integrated carbon nanotube (CNT) field emission cathodes and low-temperature co-fired ceramics (LTCC). International Journal of Mass Spectrometry. 2017 Nov 1;422:162–9.
• Kim JY, Kim J, Amsden JJ, Roh J, Park I, Yoon DY, et al. Temperature Dependence and Impedance Characteristics of Hybrid Solar Cells Based on Poly(phenylene vinylene): ZnO Nanoparticles with Added Surfactants. IEEE Journal of Photovoltaics. 2017 Jul 1;7(4):1031–5.
• Amsden JJ, Gehm ME, Russell ZE, Chen EX, Di Dona ST, Wolter SD, et al. Coded Apertures in Mass Spectrometry. Annual review of analytical chemistry (Palo Alto, Calif). 2017 Jun;10(1):141–56.
• Radauscher EJ, Gilchrist KH, Di Dona ST, Russell ZE, Piascik JR, Amsden JJ, et al. Improved Performance of Field Emission Vacuum Microelectronic Devices for Integrated Circuits. IEEE Transactions on Electron Devices. 2016 Sep 1;63(9):3753–60.
• Russell ZE, DiDona ST, Amsden JJ, Parker CB, Kibelka G, Gehm ME, et al. Compatibility of Spatially Coded Apertures with a Miniature Mattauch-Herzog Mass Spectrograph. Journal of the American Society for Mass Spectrometry. 2016 Apr;27(4):578–84.
• Mitropoulos AN, Marelli B, Perotto G, Amsden J, KapLan DL, Omenetto FG. Towards the fabrication of biohybrid silk fibroin materials: Entrapment and preservation of chloroplast organelles in silk fibroin films. RSC Advances. 2016 Jan 1;6(76):72366–70.
• Radauscher EJ, Keil AD, Wells M, Amsden JJ, Piascik JR, Parker CB, et al. Chemical ionization mass spectrometry using carbon nanotube field emission electron sources. Journal of the American Society for Mass Spectrometry. 2015 Nov;26(11):1903–10.
• Parker CB, Amsden JJ, Peng Q, Stoner BR, Glass JT. Achieving Excellence in Graduate Research: A Guide for New Graduate Students. Advanced science (Weinheim, Baden-Wurttemberg, Germany). 2015 Oct;2(10):1500203.
• Chen EX, Russell ZE, Amsden JJ, Wolter SD, Danell RM, Parker CB, et al. Order of Magnitude Signal Gain in Magnetic Sector Mass Spectrometry Via Aperture Coding. Journal of the American Society for Mass Spectrometry. 2015 Sep;26(9):1633–40.
• Russell ZE, Chen EX, Amsden JJ, Wolter SD, Danell RM, Parker CB, et al. Two-dimensional aperture coding for magnetic sector mass spectrometry. Journal of the American Society for Mass Spectrometry. 2015 Feb;26(2):248–56.
• Gilchrist KH, Piascik JR, Stoner BR, Radauscher EJ, Amsden JJ, Parker CB, et al. Platform for integrated vacuum microelectronic circuits. In: IEEE International Vacuum Electronics Conference, IVEC 2014. 2014. p. 155–6.
• Tao H, Siebert SM, Pritchard EM, Sassaroli A, Panilaitis B, Brenckle MA, et al. Implantable resorbable micro-prism arrays for real-time drug release monitoring. In: 2012 Conference on Lasers and Electro-Optics, CLEO 2012. 2012.
• Tao H, Kainerstorfer JM, Siebert SM, Pritchard EM, Sassaroli A, Panilaitis BJB, et al. Implantable, multifunctional, bioresorbable optics. Proceedings of the National Academy of Sciences of the United States of America. 2012 Nov;109(48):19584–9.
• Lee C, Kim JY, Amsden JJ, Lee D, Yoon DY. Polymer-nanoparticle hybrid solar cell. In: Technical Digest - 2012 17th Opto-Electronics and Communications Conference, OECC 2012. 2012. p. 101–2.
• Meister M, Amsden JJ, Howard IA, Park I, Lee C, Yoon DY, et al. Parallel pool analysis of transient spectroscopy reveals origins of and perspectives for ZnO hybrid solar cell performance enhancement using semiconducting surfactants. Journal of Physical Chemistry Letters. 2012 Sep 20;3(18):2665–70.
• Toffanin S, Kim S, Cavallini S, Natali M, Benfenati V, Amsden JJ, et al. Low-threshold blue lasing from silk fibroin thin films. Applied Physics Letters. 2012 Aug 27;101(9).
• Tao H, Siebert SM, Pritchard EM, Sassaroli A, Panilaitis B, Brenckle MA, et al. Implantable resorbable micro-prism arrays for real-time drug release monitoring. In: CLEO: Science and Innovations, CLEO_SI 2012. 2012.
• Kim JY, Noh S, Nam YM, Roh J, Park M, Amsden JJ, et al. Effect of nanoscale SubPc interfacial layer on the performance of inverted polymer solar cells based on P3HT/PC71BM. ACS Applied Materials and Interfaces. 2011 Nov 23;3(11):4279–85.
• White RD, Gray C, Mandelup E, Amsden JJ, Kaplan DL, Omenetto FG. Rapid nano impact printing of silk biopolymer thin films. Journal of Micromechanics and Microengineering. 2011 Nov 1;21(11).
• Noh S, Lee D, Kim JY, Park Y, Lee C, Amsden JJ. Area and light intensity dependence of buffer layers on P3HT: PCBM solar cells. Journal of the Korean Physical Society. 2011 Aug 12;59(2):207–10.
• Park I, Lim Y, Noh S, Lee D, Meister M, Amsden JJ, et al. Enhanced photovoltaic performance of ZnO nanoparticle/poly(phenylene vinylene) hybrid photovoltaic cells by semiconducting surfactant. Organic Electronics. 2011 Jan 1;12(3):424–8.
• Capelli R, Amsden JJ, Generali G, Toffanin S, Benfenati V, Muccini M, et al. Integration of silk protein in organic and light-emitting transistors. Organic Electronics. 2011 Jan 1;12(7):1146–51.
• Adato R, Yanik AA, Amsden JJ, Kaplan DL, Omenetto FG, Hong MK, et al. Radiative engineering of nanoantenna arrays for ultra-sensitive vibrational spectroscopy of proteins. In: Proceedings of SPIE - The International Society for Optical Engineering. 2010.
• Lee SY, Amsden JJ, Boriskina SV, Omenetto FG, Negro LD. Biosensing with colorimetric signatures of deterministic aperiodic metal nanoparticle arrays. In: Optics InfoBase Conference Papers. 2010.
• Adato R, Yanik AA, Amsden JJ, Kaplan DL, Omenetto FG, Hong MK, et al. Ultra-sensitive infrared spectroscopy of proteins with collective excitations of nanoplasmonic arrays. In: Optics InfoBase Conference Papers. 2010.
• Mondia JP, Amsden JJ, Lin D, Negro LD, Kaplan DL, Omenetto FG. Rapid nanoimprinting of doped silk films for enhanced fluorescent emission. Advanced materials (Deerfield Beach, Fla). 2010 Nov;22(41):4596–9.
• Tao H, Amsden JJ, Strikwerda AC, Fan K, Kaplan DL, Zhang X, et al. Metamaterial silk composites at terahertz frequencies. Advanced materials (Deerfield Beach, Fla). 2010 Aug;22(32):3527–31.
• Boriskina SV, Lee SYK, Amsden JJ, Omenetto FG, Negro LD. Formation of colorimetric fingerprints on nano-patterned deterministic aperiodic surfaces. Optics Express. 2010 Jul 5;18(14):14568–76.
• Lee SY, Amsden JJ, Boriskina SV, Gopinath A, Mitropolous A, Kaplan DL, et al. Spatial and spectral detection of protein monolayers with deterministic aperiodic arrays of metal nanoparticles. Proceedings of the National Academy of Sciences of the United States of America. 2010 Jul;107(27):12086–90.
• Kim D-H, Viventi J, Amsden JJ, Xiao J, Vigeland L, Kim Y-S, et al. Dissolvable films of silk fibroin for ultrathin conformal bio-integrated electronics. Nature materials. 2010 Jun;9(6):511–7.
• Amsden JJ, Domachuk P, Gopinath A, White RD, Negro LD, Kaplan DL, et al. Rapid nanoimprinting of silk fibroin films for biophotonic applications. Advanced materials (Deerfield Beach, Fla). 2010 Apr;22(15):1746–9.
• Adato R, Yanik AA, Amsden JJ, Kaplan DL, Omenetto FG, Hong MK, et al. Ultra-sensitive infrared spectroscopy of proteins with collective excitations of nanoplasmonic arrays. In: Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference: 2010 Laser Science to Photonic Applications, CLEO/QELS 2010. 2010.
• Tao H, Amsden JJ, Strikwerda AC, Fan K, Kaplan DL, Omenetto FG, et al. Large area spraying of terahertz materials on free-standing biocompatible silk films. In: Technical Digest - Solid-State Sensors, Actuators, and Microsystems Workshop. 2010. p. 138–41.
• Domachuk P, Perry H, Amsden JJ, Kaplan DL, Omenetto FG. Bioactive "self-sensing" optical systems. Applied Physics Letters. 2009 Dec 1;95(25).
• Kim DH, Kim YS, Amsden J, Panilaitis B, Kaplan DL, Omenetto FG, et al. Erratum: Silicon electronics on silk as a path to bioresorbable, implantable devices (Applied Physics Letters (2009) 95 (133701)). Applied Physics Letters. 2009 Dec 1;95(26).
• Amsden JJ, Gopinath A, Negro LD, Kaplan DL, Omenetto FG. Silk fibroin biosensor based on imprinted periodic nanostructures. In: Optics InfoBase Conference Papers. 2009.
• Amsden JJ, Gopinath A, Dal Negro L, Kaplan DL, Omenetto FG. Silk fibroin biosensor based on imprinted periodic nanostructures. In: 2009 Conference on Lasers and Electro-Optics and 2009 Conference on Quantum Electronics and Laser Science Conference, CLEO/QELS 2009. 2009.
• Adato R, Yanik AA, Amsden JJ, Kaplan DL, Omenetto FG, Hong MK, et al. Ultra-sensitive vibrational spectroscopy of protein monolayers with plasmonic nanoantenna arrays. Proceedings of the National Academy of Sciences of the United States of America. 2009 Nov;106(46):19227–32.
• Amsden JJ, Perry H, Boriskina SV, Gopinath A, Kaplan DL, Dal Negro L, et al. Spectral analysis of induced color change on periodically nanopatterned silk films. Optics express. 2009 Nov;17(23):21271–9.
• Kim DH, Kim YS, Amsden J, Panilaitis B, Kaplan DL, Omenetto FG, et al. Silicon electronics on silk as a path to bioresorbable, implantable devices. Applied Physics Letters. 2009 Oct 12;95(13).
• Parker ST, Domachuk P, Amsden J, Bressner J, Lewis JA, Kaplan DL, et al. Biocompatible silk printed optical waveguides. Advanced Materials. 2009 Jun 19;21(23):2411–5.
• Amsden JJ, Gopinath A, Negro LD, Kaplan DL, Omenetto FG. Silk fibroin biosensor based on imprinted periodic nanostructures. In: Optics InfoBase Conference Papers. 2009.
• Amsden JJ, Kralj JM, Bergo VB, Spudich EN, Spudich JL, Rothschild KJ. Different structural changes occur in blue- and green-proteorhodopsins during the primary photoreaction. Biochemistry. 2008 Nov;47(44):11490–8.
• Chieffo LR, Shattuck JT, Pinnick E, Amsden JJ, Hong MK, Wang F, et al. Nitrous oxide vibrational energy relaxation is a probe of interfacial water in lipid bilayers. Journal of Physical Chemistry B. 2008 Oct 9;112(40):12776–82.
• Kralj JM, Bergo VB, Amsden JJ, Spudich EN, Spudich JL, Rothschild KJ. Protonation state of Glu142 differs in the green- and blue-absorbing variants of proteorhodopsin. Biochemistry. 2008 Mar;47(11):3447–53.
• Chieffo L, Shattuck J, Amsden JJ, Erramilli S, Ziegler LD. Ultrafast vibrational relaxation of liquid H2O following librational combination band excitation. Chemical Physics. 2007 Nov 15;341(1–3):71–80.
• Amsden JJ, Kralj JM, Chieffo LR, Wang X, Erramilli S, Spudich EN, et al. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction. Journal of Physical Chemistry B. 2007 Oct 11;111(40):11824–31.
• Bergo VB, Ntefidou M, Trivedi VD, Amsden JJ, Kralj JM, Rothschild KJ, et al. Conformational changes in the photocycle of Anabaena sensory rhodopsin: absence of the Schiff base counterion protonation signal. The Journal of biological chemistry. 2006 Jun;281(22):15208–14.
• Maji SK, Amsden JJ, Rothschild KJ, Condron MM, Teplow DB. Conformational dynamics of amyloid beta-protein assembly probed using intrinsic fluorescence. Biochemistry. 2005 Oct;44(40):13365–76.
• Bergo V, Amsden JJ, Spudich EN, Spudich JL, Rothschild KJ. Structural changes in the photoactive site of proteorhodopsin during the primary photoreaction. Biochemistry. 2004 Jul;43(28):9075–83.